+Open data
-Basic information
Entry | Database: PDB / ID: 1ibq | ||||||
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Title | ASPERGILLOPEPSIN FROM ASPERGILLUS PHOENICIS | ||||||
Components | ASPERGILLOPEPSIN | ||||||
Keywords | HYDROLASE / ASPERGILLOPEPSIN / ASPARTIC PROTEINASE | ||||||
Function / homology | Function and homology information aspergillopepsin I / aspartic-type endopeptidase activity / extracellular region Similarity search - Function | ||||||
Biological species | Aspergillus phoenicis (mold) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Cho, S.W. / Shin, W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure of aspergillopepsin I from Aspergillus phoenicis: variations of the S1'-S2 subsite in aspartic proteinases. Authors: Cho, S.W. / Kim, N. / Choi, M.U. / Shin, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ibq.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ibq.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ibq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/1ibq ftp://data.pdbj.org/pub/pdb/validation_reports/ib/1ibq | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34219.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aspergillus phoenicis (mold) / References: UniProt: Q12567, aspergillopepsin I #2: Sugar | ChemComp-MAN / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1 Å3/Da / Density % sol: 41.86 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18% PEG8000, 0.1M sodium cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 Å |
Detector | Type: ENRAF-NONIUS FAST / Detector: AREA DETECTOR / Date: Jan 1, 1999 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→26.34 Å / Num. all: 88563 / Num. obs: 26402 / % possible obs: 77.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.3 % / Biso Wilson estimate: 4.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.14→2.27 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.12 / % possible all: 45.5 |
Reflection | *PLUS % possible obs: 86.6 % / Num. measured all: 88563 |
Reflection shell | *PLUS % possible obs: 43.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→26.34 Å / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.14→26.34 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.2 |